Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
Performance comparison of generalized born and Poisson methods in the calculation of electrostatic solvation energies for protein structures
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DOI：
10.1002/jcc.10378
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发表时间：
2004-01-30
影响因子：
3
通讯作者：
Brooks, CL
中科院分区：
文献类型：
--
作者：
Feig, M;Onufriev, A;Brooks, CL
本文比较了广义Born（GB）和Poisson（PB）方法计算蛋白质静电溶剂化能的结果。一个大的GB和PB的实现，从我们自己的实验室以及其他人被应用到一系列的蛋白质结构测试集，以评估这些方法的性能。测试集涵盖了不同大小、折叠拓扑结构和氨基酸组成的天然蛋白质结构的显著范围，以及在结构预测和折叠/展开研究期间可能发现的规范性延伸和错误折叠结构。我们发现，这里测试的方法范围很广，从高度准确和计算要求高的PB为基础的方法，有点不太准确，但更实惠的GB为基础的方法和一些快速，近似PB求解器。与PB溶剂化能相比，发现最新的、最准确的GB实现对于不同蛋白质之间的相对溶剂化能实现1%的误差，并且对于相同蛋白质的不同构象之间的相对溶剂化能实现0.4%的误差。这与精确的PB解算器相比，它们产生的结果对于原生结构和规范结构的偏差小于0.25%。最好的GB方法的性能进行了更详细的讨论力场为基础的最小化或分子动力学模拟的应用。
This study compares generalized Born (GB) and Poisson (PB) methods for calculating electrostatic solvation energies of proteins. A large set of GB and PB implementations from our own laboratories as well as others is applied to a series of protein structure test sets for evaluating the performance of these methods. The test sets cover a significant range of native protein structures of varying size, fold topology, and amino acid composition as well as normative extended and misfolded structures that may be found during structure prediction and folding/unfolding studies. We find that the methods tested here span a wide range from highly accurate and computationally demanding PB-based methods to somewhat less accurate but more affordable GB-based approaches and a few fast, approximate PB solvers. Compared with PB solvation energies, the latest, most accurate GB implementations were found to achieve errors of 1% for relative solvation energies between different proteins and 0.4% between different conformations of the same protein. This compares to accurate PB solvers that produce results with deviations of less than 0.25% between each other for both native and normative structures. The performance of the best GB methods is discussed in more detail for the application for force field-based minimizations or molecular dynamics simulations.